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zhangtaolab/DNALLM
Introduction
Getting Started
User Guide
API
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DNALLM Documentation
zhangtaolab/DNALLM
Introduction
Getting Started
Getting Started
Quick Start
Installation
User Guide
User Guide
Getting Started
Common Workflows
Best Practices
Performance Guide
Troubleshooting
Tutorial
Tutorial
End-to-End Workflow
Data Processing
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Fine Tuning
Fine Tuning
Overview
Getting Started
Configuration
Advanced Techniques
Task Guides
Inference
Inference
Getting Started
Basic Inference
Advanced Inference
Mutagenesis Analysis
Visualization
Performance Optimization
Benchmark
Benchmark
Overview
Getting Started
Configuration
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Examples
MCP
MCP
Configuration
Server Setup
Usage Guide
CLI Tools
CLI Tools
Overview
Usage Guide
Configuration Generator
MCP Server
Performance Optimization
Performance Optimization
GPU Optimization
Memory Optimization
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Model Quantization
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Case Studies
Case Studies
Promoter Prediction
Motif Detection
Sequence Generation
Multi-Task Learning
API
API
Overview
Configuration
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Model
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Special Models
Basenji2
Borzoi
DNABERT2
EVO
Enformer
GPN
LucaOne
LucaOne
Table of contents
lucaone
megaDNA
MutBERT
Omni-DNA
SPACE
Datahandling
Datahandling
Data
Auto Builders
Inference
Inference
Inference
Benchmark
Mutagenesis
Interpretation
Plot
Finetune
Finetune
Trainer
MCP
MCP
Server
Config Manager
Config Validators
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Tasks
Tasks
Task
Metrics
Utils
Utils
Sequence
Logger
Support
Concepts
Concepts
Biology
Biology
DNA Sequences
Genomic Features
Biological Tasks
Sequence Analysis
Training
Inference
MCP
Architecture
Architecture
Model Architectures
Tokenization
Attention Mechanisms
Embedding Layers
Technical Guides
Technical Guides
Transfer Learning
Fine-tuning Strategies
Evaluation Metrics
Performance Optimization
Resources
Resources
Model Zoo
Data Handling
Model Selection
Model Troubleshooting
Model Guides
Model Guides
BERT Models
Caduceus Models
ESM Models
Hyena Models
Llama Models
Mamba Models
EVO Models
Flash Attention Models
Special Models
Examples
Examples
Notebooks
Notebooks
Overview
Fine-Tuning
Fine-Tuning
Binary Classification
Multi-Label Classification
NER Fine-tuning
NER Data Generation
Custom Head
Generation
LoRA Fine-tuning
LoRA Inference
Inference
Inference
Basic Inference
EVO Models
MegaDNA Models
Sequence Generation
tRNA Inference
Analysis
Analysis
Mutagenesis
Interpretation
Embedding
Benchmarking
Benchmarking
Benchmark
Data Preparation
Data Preparation
Fine-tuning Data
Prediction Data Preparation
MCP Examples
MCP Examples
DNALLM MCP Client with LangChain Agents
Pydantic AI with Ollama and MCP Server
Marimo Demos
Marimo Demos
Fine-tuning Demo
Inference Demo
Benchmark Demo
FAQ
FAQ
Overview
Installation
Models
Benchmark
Fine-tuning
Data Processing
CLI
Inference
MCP
Table of contents
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